Hi Rick,

Thanks for looking at the data. After looking at just the 3dmerge output without an underlay to evaluate the number of clusters I think that my problem is more simple than I had previously believed. Is there a way to request +tlrc output from 3dmerge? When I run the 3dmerge command on a zstat from a different analysis it kicks out +tlrc and I can use the MNI template as an underlay in Afni to evaluate the clusters visually. However, with the nii.gz that I uploaded 3dmerge automatically makes the output +orig so that when I use the MNI template there is a mismatch in the view and the clusters are replaced with an unthresholded image.

I've used the same fsl feat run to create both of the nii.gz images and 3dinfo tells me they are the same dimensions. Why would 3dmerge make one +tlrc and one +orig?

Thanks again,
Rachel